Abstract: The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT®) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT® cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT® Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT® sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy.

Abstract: The invention is directed to techniques for supporting multi-link protocols within a computer network. In one embodiment, a method includes receiving a set of data blocks from a plurality of links in one or more interface cards according to a multi-link protocol and sending the data blocks to a multi-link service card for sequencing. The data blocks may then be sent to the one or more interface cards for communication to a destination device over a computer network. Implementing a multi-link service card may allow a network device, such as a router, to support multi-link protocols.

Abstract: Methods for amplifying a desired target region of a nucleic acid through rolling circle amplification with a strand-displacing polymerase are provided. Concatameric hairpin products are resolved with endonuclease digestion, and the resulting amplified product hairpins or fragments can be circularized and employed as templates in a subsequent round of amplification. The methods are effective for targeted amplification of even highly repetitive sequences. Compositions, kits, and systems related to or useful in the methods are also described.

Abstract: A process for purifying a dicarboxylic acid that is derived from the mixed oxidation products from an ozonization of a mixture containing an ethylenically unsaturated compound having between 6 to 24 carbons, the process includes distilling the mixed oxidation products to provide a first distillate, and a second distillate, where the second distillate includes the dicarboxylic acid and impurity acids, partitioning the second distillate between water and a organic solvent, separating the organic solvent layer from the water layer, lowering the temperature of the water layer to crystallize at least a portion of the dicarboxylic acid, separating the crystallized dicarboxylic acid solid, melting the crystallized dicarboxylic acid, and distilling the liquid dicarboxylic acid to provide a purified dicarboxylic acid.

Abstract: Methods for amplifying a desired target region of a nucleic acid through rolling circle amplification with a strand-displacing polymerase are provided. Concatameric hairpin products are resolved with endonuclease digestion, and the resulting amplified product hairpins or fragments can be circularized and employed as templates in a subsequent round of amplification. The methods are effective for targeted amplification of even highly repetitive sequences. Compositions, kits, and systems related to or useful in the methods are also described.

Abstract: The present invention is generally directed to a hierarchical genome assembly process for producing high-quality de novo genome assemblies. The method utilizes a single, long-insert, shotgun DNA library in conjunction with Single Molecule, Real-Time (SMRT®) DNA sequencing, and obviates the need for additional sample preparation and sequencing data sets required for previously described hybrid assembly strategies. Efficient de novo assembly from genomic DNA to a finished genome sequence is demonstrated for several microorganisms using as little as three SMRT® cells, and for bacterial artificial chromosomes (BACs) using sequencing data from just one SMRT® Cell. Part of this new assembly workflow is a new consensus algorithm which takes advantage of SMRT® sequencing primary quality values, to produce a highly accurate de novo genome sequence, exceeding 99.999% (QV 50) accuracy.

Abstract: A process for purifying a dicarboxylic acid that is derived from the mixed oxidation products from an ozonization of a mixture containing an ethylenically unsaturated compound having between 6 to 24 carbons, the process includes distilling the mixed oxidation products to provide a first distillate, and a second distillate, where the second distillate includes the dicarboxylic acid and impurity acids, partitioning the second distillate between water and a organic solvent, separating the organic solvent layer from the water layer, lowering the temperature of the water layer to crystallize at least a portion of the dicarboxylic acid, separating the crystallized dicarboxylic acid solid, melting the crystallized dicarboxylic acid, and distilling the liquid dicarboxylic acid to provide a purified dicarboxylic acid.

Abstract: A method for performing multilink communications may include applying a quality-of-service (QoS) policy to incoming traffic, where the QoS policy operates to identify a first portion and a second portion of the incoming traffic. The method may include fragmenting the first portion of the incoming traffic into a group of fragments. The method may include sequencing the group of fragments and the second portion of the incoming traffic into a sequenced flow, where the sequencing causes the second portion to be interleaved among the group of fragments so that the sequenced flow can be made available to a first link and a second link as multilink traffic, where the first link carries a first portion of the multilink traffic and the second link carries a second portion of the multilink traffic.

Abstract: A method for performing multilink communications may include applying a quality-of-service (QoS) policy to incoming traffic, where the QoS policy operates to identify a first portion and a second portion of the incoming traffic. The method may include fragmenting the first portion of the incoming traffic into a group of fragments. The method may include sequencing the group of fragments and the second portion of the incoming traffic into a sequenced flow, where the sequencing causes the second portion to be interleaved among the group of fragments so that the sequenced flow can be made available to a first link and a second link as multilink traffic, where the first link carries a first portion of the multilink traffic and the second link carries a second portion of the multilink traffic.

Abstract: A network router includes a set of interface cards to receive packets from a network, and a set of accounting modules to calculate flow statistics for the packets. The router further includes a control unit to adaptively update routing information in response to the calculated flow statistics, and to route the packets in accordance with the routing information. The control unit identifies potentially malicious packet flows for the received packets based on the flow statistics, and applies an intercept filter to intercept the packets of the identified packet flows. The control unit analyzes the intercepted packets in real-time to determine the presence of a network event, and updates the routing information based on the determination, e.g., by terminating routing for packets associated with malicious packet flows. In this manner, the router may adaptively respond to network events, such as network security violations.

Abstract: Separation of long molecules by length is obtained by forcing such molecules to traverse a boundary between a low free-energy region and a high free-energy region. In one embodiment, the high free-energy region is a dense pillar region or other structure formed on a semiconductor substrate. One or more membranes are used in further embodiments. The low free-energy region is a larger chamber formed adjacent the high free-energy region. A recoil phase allows longer molecules not fully driven into the high free-energy region to recoil into the low free-energy region. In a further variation, the high free-energy region is a membrane having nanoscale holes.

Abstract: A network device integrates accounting functionality for generation of flow statistics with packet intercept functionality to provide a comprehensive traffic analysis environment. The device comprises a set of network interface cards to receive packets from a network, and a set of accounting service cards to calculate flow statistics for the packets. The device further comprises a control unit to receive the network packets from the interface cards and distribute the packets to the set of accounting service cards. The accounting service card comprises an interface for insertion within a slot of a network device. Accounting service cards may be added to easily scale the network device to support higher bandwidth communication links, such as OC-3, OC-12, OC048 and higher rate links. Additional accounting service cards may be used for purposes of redundancy to support continuous, uninterrupted packet processing and accounting in the event of a card failure.

Abstract: A network router includes a set of interface cards to receive packets from a network, and a set of accounting modules to calculate flow statistics for the packets. The router further includes a control unit to adaptively update routing information in response to the calculated flow statistics, and to route the packets in accordance with the routing information. The control unit identifies potentially malicious packet flows for the received packets based on the flow statistics, and applies an intercept filter to intercept the packets of the identified packet flows. The control unit analyzes the intercepted packets in real-time to determine the presence of a network event, and updates the routing information based on the determination, e.g., by terminating routing for packets associated with malicious packet flows. In this manner, the router may adaptively respond to network events, such as network security violations.

Abstract: A microfluidic device has features that reduce the speed of flow of higher speed diffusing molecules. The features are used to separate various components of a mixture in the microfluidic device. The channel is sized to ensure laminar flow of the mixture to promote only diffusive mixing of the components. Wells extend from the channel. Components having higher diffusing velocities are slowed by the wells as the mixture proceeds through the channel. The result is that slower speed diffusing components exit the channel prior to the lower speed diffusing components. The device is formed by use of photolithographic techniques or other techniques capable of forming such features.

Abstract: Composition, systems, apparatus and methods of enhancing fluorescent signals in biochemical are described. Metal particle proximity to enzymes that produce fluorescent products provide enhanced fluorescence of the product and plasmon resonance of the metal particle. Multi-labeled nucleotides enhance signal production. Reflectance of illumination light and emitted fluorescence increase signal strength for a given illumination light.

Abstract: Separation of long molecules by length is obtained by forcing such molecules to traverse a boundary between a low free-energy region and a high free-energy region. In one embodiment, the high free-energy region is a dense pillar region or other structure formed on a semiconductor substrate. One or more membranes are used in further embodiments. The low free-energy region is a larger chamber formed adjacent the high free-energy region. A recoil phase allows longer molecules not fully driven into the high free-energy region to recoil into the low free-energy region. In a further variation, the high free-energy region is a membrane having nanoscale holes.

Abstract: A network device integrates accounting functionality for generation of flow statistics with packet intercept functionality to provide a comprehensive traffic analysis environment. The device comprises a set of network interface cards to receive packets from a network, and a set of accounting service cards to calculate flow statistics for the packets. The device further comprises a control unit to receive the network packets from the interface cards and distribute the packets to the set of accounting service cards. The accounting service card comprises an interface for insertion within a slot of a network device. Accounting service cards may be added to easily scale the network device to support higher bandwidth communication links, such as OC-3, OC-12, OC048 and higher rate links. Additional accounting service cards may be used for purposes of redundancy to support continuous, uninterrupted packet processing and accounting in the event of a card failure.

Abstract: The present invention is directed to a method and an apparatus for analysis of an analyte. The method involves providing a zero-mode waveguide which includes a cladding surrounding a core where the cladding is configured to preclude propagation of electromagnetic energy of a frequency less than a cutoff frequency longitudinally through the core of the zero-mode waveguide. The analyte is positioned in the core of the zero-mode waveguide and is then subjected, in the core of the zero-mode wave guide, to activating electromagnetic radiation of a frequency less than the cut-off frequency under conditions effective to permit analysis of the analyte in an effective observation volume which is more compact than if the analysis were carried out in the absence of the zero-mode waveguide.

Abstract: A network router integrates routing functionality with accounting functionality for generation of flow statistics, and provides packet intercept functionality to provide a comprehensive traffic analysis environment. The router includes a set of interface cards to receive packets from a network, and a control unit to generate a first and second duplicate stream of the packets. The control unit provides the packets of the first stream to accounting modules for calculation of flow statistics, and applies an intercept filter to intercept at least a subset of the packets of the second stream for selected packet flows.

Abstract: A network router includes a set of interface cards to receive packets from a network, and a set of accounting modules to calculate flow statistics for the packets. The router further includes a control unit to adaptively update routing information in response to the calculated flow statistics, and to route the packets in accordance with the routing information. The control unit identifies potentially malicious packet flows for the received packets based on the flow statistics, and applies an intercept filter to intercept the packets of the identified packet flows. The control unit analyzes the intercepted packets in real-time to determine the presence of a network event, and updates the routing information based on the determination, e.g., by terminating routing for packets associated with malicious packet flows. In this manner, the router may adaptively respond to network events, such as network security violations.